Open ranjaniramesh99 opened 1 month ago
Hey, the mismatch must have happened already during prediction... what is the image size of the original predicted image? Best, Constantin
Hi, Thanks for your prompt reply! The size was (1,83,159,99). Thanks!
Thats really strange and should not happen. Are you allowed to share your data?
Just to be clear, I ran c3d on the predicted and ground truth and Dice was fine. The headers/size look identical. The error happens when using the evaluator.
So basically when the evaluator loads both the prediction and the GT, it changes shapes? Did you validate that?
We will check that and get back.
Hi, I was interested to evaluate the dice score on my test data and ground data and was facing an issue about an image size mismatch. What would you recommend I do in this case?
Attaching the detailed error for your reference below: Using <class 'nnunetv2.imageio.simpleitk_reader_writer.SimpleITKIO'> reader/writer multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/usr/lib/python3.10/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/usr/lib/python3.10/multiprocessing/pool.py", line 51, in starmapstar return list(itertools.starmap(args[0], args[1])) File "/usr/local/lib/python3.10/dist-packages/nnunetv2/evaluation/evaluate_predictions.py", line 107, in compute_metrics tp, fp, fn, tn = compute_tp_fp_fn_tn(mask_ref, mask_pred, ignore_mask) File "/usr/local/lib/python3.10/dist-packages/nnunetv2/evaluation/evaluate_predictions.py", line 82, in compute_tp_fp_fn_tn tp = np.sum((mask_ref & mask_pred) & use_mask) ValueError: operands could not be broadcast together with shapes (1,85,161,101) (1,83,159,99) """
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/usr/local/bin/nnUNetv2_evaluate_folder", line 8, in
sys.exit(evaluate_folder_entry_point())
File "/usr/local/lib/python3.10/dist-packages/nnunetv2/evaluation/evaluate_predictions.py", line 232, in evaluate_folder_entry_point
compute_metrics_on_folder2(args.gt_folder, args.pred_folder, args.djfile, args.pfile, args.o, args.np, chill=args.chill)
File "/usr/local/lib/python3.10/dist-packages/nnunetv2/evaluation/evaluate_predictions.py", line 196, in compute_metrics_on_folder2
compute_metrics_on_folder(folder_ref, folder_pred, output_file, rw, file_ending,
File "/usr/local/lib/python3.10/dist-packages/nnunetv2/evaluation/evaluate_predictions.py", line 145, in compute_metrics_on_folder
results = pool.starmap(
File "/usr/lib/python3.10/multiprocessing/pool.py", line 375, in starmap
return self._map_async(func, iterable, starmapstar, chunksize).get()
File "/usr/lib/python3.10/multiprocessing/pool.py", line 774, in get
raise self._value
ValueError: operands could not be broadcast together with shapes (1,85,161,101) (1,83,159,99)
Thanks!